/*
#Copyright (c) 2013, Philippe Bordron <philippe.bordron@gmail.com>
#
# This file is part of SIPPER.
#
# DCC is free software: you can redistribute it and/or modify
# it under the terms of the GNU LESSER GENERAL PUBLIC LICENSE as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# DCC is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU LESSER GENERAL PUBLIC LICENSE for more details.
#
# You should have received a copy of the GNU LESSER GENERAL PUBLIC LICENSE
# along with SIPPER.  If not, see <http://www.gnu.org/licenses/>
*/
package combi.sipper.modeling.distances;

import combi.wip.sipper.modeling.Protein;
import combi.wip.sipper.modeling.genomes.Gene;
import combi.wip.sipper.modeling.genomes.Genome;

public class DistanceColocalisation<G extends Gene<E>, E extends Protein> implements DistanceBetweenGenes<G> {

	private Genome<G, E> genome;
	public DistanceColocalisation(Genome<G, E> genome)
	{
		this.genome = genome;
	}
	
	@Override
	public double get(G g1, G g2) {
		double result = defaultResult;
		if (genome.contains(g1) && genome.contains(g2))
		{
			result = Math.abs(genome.getRank(g1)-genome.getRank(g2));
			result = Math.min(genome.size()-result, result);
		}
		return result;
	}
}
